Andrew7dg,
I actually had to do the same thing on my truck. It looks like you are on to the right track with the repair. I went ahead and ordered new inner and outer roof panels and replaced both. I basically just followed the seams of the panels from the factory and drilled out all of the spot welds, cut along the brazed joints on the A-pillars, and removed the panels in two big pieces.
Not sure if it's too late by now, but I would suggest mounting the doors before you cut out the inner roof panel. This gave me a good reference on fitment when I was putting the new roof together and making sure the top of door gaps were somewhat correct. Definitely put some kind of paint on the inside of the panels before you weld everything back up, I just put two coasts of epoxy primer on them. Another thing I did before welding the outer roof panel on was to run new dome light, and speaker wires up the A-piller and to their respective locations. I figured this would be the easiest time to do that with everything open and easy to place the new wires. I also lined the underside of the outer panel with Dynamat and Dynaliner. No idea if both were necessary, expensive...sure a little, but this project is stretching out over a long period of time so cost wasn't too big a deal to me.
For me this was the most daunting work to do on the cab initially, but turned out to be one of the easiest jobs to do.
Here are some pictures from my project doing the roof swap:
1957 GMC Roof Swap
